The Sierra Nevada red fox (Vulpes vulpes necator) occurred historically throughout the high elevations of California's Sierra Nevada and southern Cascade Mountains. Before this study, the only known remaining population in California consisted of ≤ 20 individuals restricted to the Lassen Peak region in the southern Cascades. In August 2010, we photographed a red fox in the Sonora Pass area of the Sierra Nevada, > 100 km from the Lassen Peak region. To determine if multiple individuals were present and were indigenous, we set up additional camera stations, collected genetic samples (saliva, scat, hair, and a carcass), and conducted a comparative genetic analysis between these individuals and historical and modern reference samples. Photo-detections identified at least three individuals based on pelage characteristics. Genetic analyses identified two females and one male, whose microsatellite profiles suggested they were closely related. A genetic assignment analysis indicated that all three individuals clustered most closely (> 95%) with historical samples from the Sierra Nevada, and were distinct from those in the Lassen Peak region. Additionally, mtDNA and microsatellite alleles unique to each population confirmed that the Sonora Pass individuals represent a second remnant California population of Sierra Nevada red fox. Reduced genetic diversity relative to historical levels in both remnant populations was consistent with small populations. Follow-up surveys are needed to determine the abundance and distributional extent of the Sonora Pass population, combined with research on both populations to assess demographic trajectories, determine threats, and to inform conservation efforts.